Sent to CCL by: "Leif Olson" [leif.olson,,kodak.com]
Hi CCL people,
I know this is similar to previous questions that have been sent to
the list in the past. But I am going to ask it anyway...I keep searching for a
program that will make simple publication quality molecular graphics pictures
(usually black-and-white), but with a couple of added features, and runs on
Windows or Linux.
Vast numbers of molecular graphics programs are advertised for their capability
to make "publication quality" images. But what this always seems to
refer to is the ability to create stunning color pictures complete with shadows,
fog effects, dramatic backgrounds, etc., perhaps rendered with the help of
POV-Ray. Nice, but not what I usually need for figures to put into journal
articles or technical reports. I usually just want ball-and-stick,
black-and-white (or a simple color scheme to highlight heteroatoms), maybe some
cross-hatching to suggest depth, and some labeling capability, with the end
result a high-resolution image or vector output.
An example of a program that comes pretty close to what I would like is
XChemEdit, where I can read in a structure, and quickly rotate/translate it to a
desired orientation. Then, with a few mouse clicks I can remove undesired
bonds, make dashed bonds (e.g. for hydrogen bonds or transition states), label
bond distances/angles/dihedrals, resize and move labels, etc. This only takes a
minute or two, unfortunately the resulting images are not, in my opinion, good
enough for external publication. They are nicely labeled and clear, but
low-resolution.
As an alternative, I have tried Schakal99, which can make excellent
publication-quality b/w molecular graphics, and it seems that one has extensive
control over the final image. But I find it difficult to use even after
studying the manual and going through quite a few examples, and I am not sure
that certain things like labeling bond angles can even be done.
I have also looked at XBS, Molden, ORTEP, and WebLab Viewer, but they aren't
quite what I am looking for either. We don't own Cache, Chem3D, or Gaussview,
so I haven't tried them...what about those or other software? Is it best to
just put in the time to really learn Schakal usage? Would you agree that fancy
photorealistic "publication quality" graphics are often discouraged by
journal editors anyway?
Thanks!
Leif Olson
Eastman Kodak Research Laboratories>